During a battle with Shredder, Leonardo, his brothers, Splinter, Shredder and a large number of Foot Ninja were all transported to a different dimension. When Shredder kidnapped Dr. Naveen Khan and began stealing equipment to build a portal between worlds, Leonardo and his brothers attempted to stop them.
These attempts brought them to the attention of Batman, who soon found and fought the Turtles. Leonardo was the last to face him individually, and though Batman broke his katanas with one of Raphael's sai, Leonardo continued fighting with his hands and feet. Afterwards, Leonardo said that Batman fought "like a detective."
Leonardo followed his father to the Bat-Cave, learning on the way there that the dimension itself was causing the mutagen in their bodies to become inert. Batman became sympathetic to their cause upon listening to Splinter's description of their plight and their enemies, and promised to get them home that very night. Unfortunately, Shredder destroyed Dr. Khan and the dimensional portal to keep his mortal foes from being able to return home.
Leonardo continued to practice his martial arts with Batman in the Bat-Cave, until an outburst from Raphael caused Batman to leave. When an alert sounded, Leonardo led his other two brothers to where Casey Jones had been left, after having canisters of mutagen taken by Shredder and Ra's al Ghul. He and Raphael accompanied Batman to speak with Commissioner Gordon, but Leonardo collapsed shortly afterwards due to the mutagen in his body reverting.
Despite his ailment, Leonardo insisted that he and his family needed to stop Shredder. When Batman was captured and threatened by a number of newly-mutated enemies, he and his brothers chose to save the superhero rather than going back to their own world. Leonardo fought with Ra's al Ghul, leading his brothers to defeat the powerful ninja. After their victory was assured, April O'Neil and Casey Jones appeared, having risked their lives to open a portal to Batman's world. Leonardo and his family returned to their own dimension.
After the imprisonment of the Shredder, Leonardo and his brothers tried to deal with the internal strife of the fracturing Foot Clan. He led them in a subterranean attack to save Oroku Karai, but they quickly had to retreat when one of the Foot Elite nearly killed Donatello.
After Bane appeared in New York, Leonardo led Raphael and Michelangelo in trying to stop the chaos, while believing that Donatello had been kidnapped by the Foot Clan. When Donatello returned with Batman and Robin, Leonardo was overjoyed, then shocked when he learned that Donatello had inadvertently caused the current situation.
He and Splinter accompanied Batman to spy on Bane, shortly before they led a mission into the Foot Clan's laboratories. It turned out to be a trap, and the group were offered a chance to kneel before Bane and serve him. In the resulting fight, Splinter was badly wounded, causing Leonardo to look to Batman for guidance.
When Donatello argued in favor of the Turtles synthesizing and using Venom themselves, Leonardo vetoed it, and spent the night strategizing with Batman. Upon discovering that Donatello had taken Venom and gone on a vengeful rampage, Leonardo and Batman tracked him down and managed to talk him out of his grief and rage. He told his brother that if he used his brains, they could defeat all of the Foot Clan at once.
He, his brothers, Nightwing, Batgirl and Robin were all brought to Liberty Island in the Turtle Van, and catapulted into the midst of the newly de-Venomed Foot Clan. Leonardo fought continuously until the Shredder arrived and disrupted Bane's power. After that, Leonardo fought Rocksteady and Bebop before being briefly knocked back by Bane. Upon Bane's defeat by Donatello, the Turtles were victorious.
Before the Bat-family's departure, Leonardo posed for a group photo with his friends and family.